Question about the SV pipeline

[mldmort]

Hi Philipp,

I have a question about this pipeline. In the bed_from_bam rule you use bamref2bed, which I assume generates a bed file from the mapped bam file. Then you use this bed file to filter the Sniffles SV calls. Two questions:

• I could not find bamref2bed program online. Is it in a python package you got from Conda? Can you provide a reference?
• Why do you need to filter the SVs with this bed file? What is the purpose of that?

Thanks a lot for clarifying. Best regards, M

[a-slide]

bamref2bed is actually in lib folder sniffles_bamref2bed.py. My understanding is that it just generates a bed formatted list with the length of each chromosome. I am not sure I understand very well the subsequent steps of filter_region and reformat_vcf.

@philres or @bsipos, would you mind clarifying ?

Thanks